Bioconductor Saturn

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IsoformSwitchAnalyzeR satuRn

22 months ago jbono ▴ 10

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Comment: competitive enrichment test yields too few significant results, self-contained t by Gordon Smyth 52k

`fry()` is a generic function with a method for DGEList objects, see `?fry.DGEList`. It doesn't convert to logCPMs but uses another edgeR-s…

Comment: competitive enrichment test yields too few significant results, self-contained t by ATpoint ★ 4.9k

Does it make sense to give the DGEList `y` to fry (or camera, roast etc) directly? It expects logcpms, so I would assume that you should be…

Comment: Should Xenium pseudobulk experiments be analysed like microarrays (limma) or lik by ATpoint ★ 4.9k

The fact that probes are used is not the deciding factor, it is how the actual gene expression is measured. Arrays hybridize probes, indeed…

Comment: competitive enrichment test yields too few significant results, self-contained t by bbao ▴ 10

That makes sense!

Comment: competitive enrichment test yields too few significant results, self-contained t by bbao ▴ 10

Hi ATpoint, I added my code in the comment below. Would appreciate any pointers if you see any glaring errors!

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